Darshan K, Aggarwal Rashmi, Bashyal Bishnu Maya, Singh Jagmohan, Shanmugam V, Gurjar Malkhan S, Solanke Amolkumar U
Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
ICAR-National Institute for Plant Biotechnology, ICAR-IARI, New Delhi, India.
Front Microbiol. 2020 Dec 7;11:578115. doi: 10.3389/fmicb.2020.578115. eCollection 2020.
Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by . Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of strain Cg2 during interaction with isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20-22 million reads with 50-58% GC. assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2-BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in "catalytic activity" constituted 45.06%, of which 10.02% were associated with "hydrolytic activity" (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in "metabolic activity" (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), -hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of against . It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the draft genome.
昆泽菌被认为是一种潜在的可防治由[病原体名称缺失]引起的小麦条斑病的生防真菌。其生物防治活性的分子机制以及所涉及的生物合成途径尚未阐明。在此，利用RNA测序对菌株Cg2与分离株BS112相互作用期间进行了全转录组分析，以便深入了解其潜在的拮抗机制。Illumina HiSeq平台（2×150 bp）平均产生2000 - 2200万条读数，GC含量为50 - 58%。组装产生了45582个转录本，其中有27957个单基因。转录组分析显示在相互作用（Cg2 - BS112）中有明显不同的表达谱，其中存在6109个独特的差异表达基因。分类为参与“催化活性”的主要转录本占45.06%，其中10.02%与“水解活性”（GO:0008152）相关，同样，在生物学过程中，29.18%的转录本参与“代谢活性”（GO:0004096和GO:0006979）。热图和聚类分类表明，编码聚酮合酶（GO:0009058）、羟甲基谷胱甘肽脱氢酶（GO:0006069）、萜烯环化酶（EC 4.2.3.-）、含氨基转移酶1_2结构域的蛋白质（GO:0009058）等次生代谢产物的基因以及其他水解性碳水化合物活性酶（CAZYmes）如糖基水解酶（GH）家族（GH 13、GH 2、GH 31和GH 81；GO:0005975）、含纤维素酶结构域的蛋白质、几丁质酶、β - 1,3 - 葡聚糖酶（GO:0004565）、葡聚糖内切 - 1,3 - β - 葡聚糖酶（GO:0052861）和蛋白酶（GO:0004177）的基因表达水平增加。使用20个随机选择的基因通过RT - qPCR对获得的RNA测序数据进行了验证，结果与RNA测序结果一致。目前的工作是全球首次揭示[昆泽菌名称缺失]对[病原体名称缺失]的生物防治机制的努力。它生成了一个新的数据集用于进一步研究，并有助于改进[昆泽菌名称缺失]基因组草图中的基因注释模型。
